Support the car as if it was sitting on it's suspension. Anything else will give you a false reading. If you get the gap looking good then set the car down the gap will close. Supported in the center the front and rear hang low opening the upper door gap. If you put a full rocker in, it goes between the inner rocker and the inner front quarter piece. That may have moved as well. In the pic below the line of at the top of the rocker. Drilling that panel and the door post loose will allow everything to move and the rear to drop significantly if you did it that way. AMD stuff is far from OEM also.
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